Variant report

Variant	rs2499957
Chromosome Location	chr11:5036384-5036385
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	11:5018576-5020673..11:5033143-5038367	GM12878	blood:
2	11:5033143-5038367..11:5566274-5571131	Hela-S3	cervix:
3	11:5033143-5038367..11:5243048-5250847	Hela-S3	cervix:
4	11:5033143-5038367..11:5250847-5268367	Hela-S3	cervix:
5	11:5033143-5038367..11:5363591-5368290	Hela-S3	cervix:
6	11:4778081-4789138..11:5033143-5038367	K562	blood:
7	11:5033143-5038367..11:5700314-5707362	K562	blood:
8	11:4789513-4794705..11:5033143-5038367	K562	blood:
9	11:5033143-5038367..11:5721056-5732713	GM12878	blood:
10	11:5033143-5038367..11:5714465-5718134	Hela-S3	cervix:
11	11:5033143-5038367..11:5600743-5604452	Hela-S3	cervix:
12	11:5033143-5038367..11:5527719-5533869	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000132256	Chromatin interaction
ENSG00000187747	Chromatin interaction
ENSG00000176798	Chromatin interaction
ENSG00000132274	Chromatin interaction
ENSG00000223609	Chromatin interaction
ENSG00000188069	Chromatin interaction
ENSG00000244734	Chromatin interaction
ENSG00000221031	Chromatin interaction
ENSG00000229988	Chromatin interaction
ENSG00000167346	Chromatin interaction
ENSG00000175520	Chromatin interaction
ENSG00000181616	Chromatin interaction
ENSG00000242180	Chromatin interaction
ENSG00000260629	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10768533	0.85[CEU][hapmap]
rs10837269	1.00[JPT][hapmap]
rs1378741	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1378744	0.93[JPT][hapmap]
rs1378745	1.00[JPT][hapmap]
rs1455962	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs1455964	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1455965	1.00[JPT][hapmap]
rs1455966	0.93[JPT][hapmap]
rs1840637	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2219231	0.93[JPT][hapmap]
rs2257785	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2412468	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2442410	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2442412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2442413	0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2442414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2442415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2445266	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2445267	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2445268	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2445269	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2445270	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2445280	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2445284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2445299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2445300	0.89[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2445302	0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2445303	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2445339	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2445340	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2445341	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2445342	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2445343	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2445344	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2499968	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2499970	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2499993	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2499994	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2499996	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2499997	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2499998	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2499999	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2500000	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2500001	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2500003	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2500010	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2500016	0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2500017	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2500018	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2500019	0.89[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2959185	0.89[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4144717	0.93[JPT][hapmap]
rs6578550	1.00[JPT][hapmap]
rs884146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	esv2758254	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	esv2759799	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv526998	chr11:4954607-5074301	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1046693	chr11:4958462-5177455	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv540938	chr11:4958462-5177455	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	esv2760169	chr11:4961518-5233821	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
8	nsv1037991	chr11:4983908-5036608	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv540939	chr11:4983908-5036608	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1042452	chr11:5000771-5036608	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv540940	chr11:5000771-5036608	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv553219	chr11:5026200-5214413	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2499957	TRIM68	cis	cerebellum	SCAN
rs2499957	OR52E4	cis	cerebellum	SCAN
rs2499957	OR52K1	cis	parietal	SCAN
rs2499957	OR10A3	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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